CVS changes by file

branch to review (2009-08-04 to 2009-08-10) v212

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.75 lines changed: 73, context: html, text, full: html, text
    add Sulf_isla strains and Stap_hell
  • 1.74 lines changed: 1, context: html, text, full: html, text
    add Pub id for mycoTube_H37Rv
  • 1.73 lines changed: 8, context: html, text, full: html, text
    add multiz and phylo for Mycobacterium
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.39 lines changed: 1, context: html, text, full: html, text
    add 'Isolation publication not available' to desc page when paper doesn't exist
• src/hg/archaeStuff/scripts/make-genome-info
  • 1.18 lines changed: 1, context: html, text, full: html, text
    reverse changes to r 1.16
  • 1.17 lines changed: 1, context: html, text, full: html, text
    capture accession number CP... and AL...
• src/hg/encode/validateFiles/makefile
  • 1.2 lines changed: 8, context: html, text, full: html, text
    add some tests
• src/hg/encode/validateFiles/validateFiles.c
  • 1.25 lines changed: 1, context: html, text, full: html, text
    change printf to verbose
  • 1.24 lines changed: 14, context: html, text, full: html, text
    more mismatch tweaks
  • 1.23 lines changed: 47, context: html, text, full: html, text
    add options to ignore N's in mismatching and to deal more efficiently with sorted files (assuming there are a lot of records)
  • 1.22 lines changed: 3, context: html, text, full: html, text
    properly deal with the N word
• src/hg/featureBits/featureBits.c
  • 1.55 lines changed: 3, context: html, text, full: html, text
    add JK's explanation of enrichment
• src/hg/gsid/gsidTable/gsidTable.c
  • 1.42 lines changed: 110, context: html, text, full: html, text
    Added logic to handle missing immuno data.
• src/hg/hgCustom/hgCustom.c
  • 1.130 lines changed: 4, context: html, text, full: html, text
    Added a note about putting bigBed and bigWig urls in a track line.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.496 lines changed: 2, context: html, text, full: html, text
    Adding level 1-3 cage track data for evaluation
• src/hg/hgTracks/hgTracks.c
  • 1.1586 lines changed: 5, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/hg/hgc/hgc.c
  • 1.1565 lines changed: 10, context: html, text, full: html, text
    Avoid Ensembl protein out link when non-coding gene
  • 1.1564 lines changed: 4, context: html, text, full: html, text
    Put ORegAnno links back in
• src/hg/inc/hvGfx.h
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinOVBio.ra
  • 1.1 lines changed: 9, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAopen.ra
  • 1.4 lines changed: 24, context: html, text, full: html, text
    Updated clinical set for open access OV datasets.
• src/hg/js/cpJsFiles.pl
  • 1.2 lines changed: 9, context: html, text, full: html, text
    workaround cp -p problem
  • 1.1 lines changed: 82, context: html, text, full: html, text
    initial checkin
• src/hg/lib/hvGfx.c
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/hg/makeDb/doc/canFam2.txt
  • 1.22 lines changed: 44, context: html, text, full: html, text
    Documented production of zebrafish danRer5 chains, nets and downloads.
• src/hg/makeDb/doc/danRer5.txt
  • 1.17 lines changed: 15, context: html, text, full: html, text
    Documented production of dog canFam2 chains, nets and downloads.
• src/hg/makeDb/doc/danRer6.txt
  • 1.7 lines changed: 12, context: html, text, full: html, text
    fixing chainself downloads
  • 1.6 lines changed: 103, context: html, text, full: html, text
    chainSelf
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.13 lines changed: 39, context: html, text, full: html, text
    Update hg18 to v54, and reset hgFixed entries to work properly for v55
• src/hg/makeDb/doc/tetNig2.txt
  • 1.4 lines changed: 166, context: html, text, full: html, text
    make Human Proteins track. Needs re-doing to deal with chrUn correctly
  • 1.3 lines changed: 21, context: html, text, full: html, text
    Set blat server and default position
  • 1.2 lines changed: 150, context: html, text, full: html, text
    Through masking and Ensembl v55 genes loaded
  • 1.1 lines changed: 42, context: html, text, full: html, text
    Download sequence tetNig2 browser build
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.346 lines changed: 15, context: html, text, full: html, text
    Added tetNig2
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.83 lines changed: 1, context: html, text, full: html, text
    Turned on genbank updates for new yeast.
• src/hg/makeDb/schema/all.joiner
  • 1.730 lines changed: 1, context: html, text, full: html, text
    added loxAfr3 to chain/nets
  • 1.729 lines changed: 9, context: html, text, full: html, text
    Adding loxAfr3
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.409 lines changed: 130, context: html, text, full: html, text
    Adding level 1-3 cage track data for evaluation
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.483 lines changed: 1, context: html, text, full: html, text
    Tweak ENCODE track label
  • 1.482 lines changed: 2, context: html, text, full: html, text
    changing download format to bedGraph
  • 1.481 lines changed: 6, context: html, text, full: html, text
    another typo.... darned Mondays
  • 1.480 lines changed: 6, context: html, text, full: html, text
    oops... fix a typo in dataSubmitted and dataRestricted
  • 1.479 lines changed: 6, context: html, text, full: html, text
    fix up dates for HudsonalphaCnv track. Also change dataType to CNV
  • 1.478 lines changed: 12, context: html, text, full: html, text
    have everything right (methinks) except dates and dataType for HA CNV tracks
  • 1.477 lines changed: 36, context: html, text, full: html, text
    added some HudsonAlphaCNV stuff... not quite done but need to test something
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Add credit to ENCODE track
  • 1.2 lines changed: 35, context: html, text, full: html, text
    changes from Kate
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    changed first person to passive voice. English teachers everywhere feel a tremour in the force.
  • 1.10 lines changed: 1, context: html, text, full: html, text
    changed red to orange for methyl calls
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.html
  • 1.10 lines changed: 26, context: html, text, full: html, text
    changed first person to passive voice. English teachers everywhere feel a tremour in the force.
  • 1.9 lines changed: 2, context: html, text, full: html, text
    fixed publication date
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Fixed typo.
• src/hg/makeDb/trackDb/makefile
  • 1.274 lines changed: 1, context: html, text, full: html, text
    Adding tetNig2 to the browser build
• src/hg/makeDb/trackDb/orangutan/ponAbe2/description.html
  • 1.5 lines changed: 3, context: html, text, full: html, text
    WUSTL links have changed
• src/hg/makeDb/trackDb/sloth/choHof1/description.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    WUSTL has changed their URL locations for assemblies
• src/hg/protein/pbGlobal/pbGlobal.c
  • 1.46 lines changed: 3, context: html, text, full: html, text
    Changed errAbort() to hUserAbort().
• src/hg/protein/pbTracks/pbTracks.c
  • 1.58 lines changed: 4, context: html, text, full: html, text
    Changed errAbort() to hUserAbort().
• src/hg/tcga/scripts/segToBed15.py
  • 1.1 lines changed: 195, context: html, text, full: html, text
    initial commit
• src/hg/utils/automation/Encode.pm
  • 1.44 lines changed: 1, context: html, text, full: html, text
    July freeze close-out
• src/hg/utils/automation/EnsGeneAutomate.pm
  • 1.19 lines changed: 21, context: html, text, full: html, text
    Add version 54 for hg18 to get it to its last version
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.24 lines changed: 16, context: html, text, full: html, text
    Trim down the gold and gap initial trackDb.ra entries
  • 1.23 lines changed: 6, context: html, text, full: html, text
    Adding chrM entry to the AGP file
• src/hg/utils/automation/n50.pl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    improved comment, minor change
  • 1.1 lines changed: 75, context: html, text, full: html, text
    Calculate N50 values from two column sizes files
• src/hg/utils/gapToLift/gapToLift.c
  • 1.8 lines changed: 18, context: html, text, full: html, text
    Properly output lift and bed lines for chroms that have no gaps
• src/inc/common.mk
  • 1.67 lines changed: 13, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/inc/memgfx.h
  • 1.25 lines changed: 13, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/inc/vGfx.h
  • 1.14 lines changed: 6, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/lib/bbiRead.c
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Fixed integer overflow that was causing right half of display to be empty at some zoom values. Added back a comment that got deleted as well.
• src/lib/htmshell.c
  • 1.61 lines changed: 12, context: html, text, full: html, text
    fixed problem where warnBox has text with display:none but doing select-all in browser (ctrl-a) selects this extra text even when there is no warning which messes up the clipboard with extra junk
• src/lib/makefile
  • 1.154 lines changed: 2, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/lib/pngwrite.c
  • 1.1 lines changed: 114, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/lib/pslGenoShow.c
  • 1.8 lines changed: 5, context: html, text, full: html, text
    use width 60 for protein codons, and 50 for nucleotides
• src/lib/pslShow.c
  • 1.10 lines changed: 5, context: html, text, full: html, text
    use width 60 for protein codons, and 50 for nucleotides
• src/lib/vPng.c
  • 1.1 lines changed: 65, context: html, text, full: html, text
    Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF. Currently used (conditionally!) only for hgTracks' main image. This is to support Tim's enhancements for horizontal scrolling of the browser track image. Image file size also appears smaller than GIF but should try more test cases.
• src/parasol/paraHub/paraHub.c
  • 1.131 lines changed: 1, context: html, text, full: html, text
    fix problem addJob with sickBatch leaving batch on curBatches instead of oldBatches
• src/parasol/parasol/parasol.c
  • 1.47 lines changed: 2, context: html, text, full: html, text
    detect and report apparent sick batch
• src/parasol/version.doc
  • 1.45 lines changed: 2, context: html, text, full: html, text
    detect and report apparent sick batch
  • 1.44 lines changed: 3, context: html, text, full: html, text
    fix problem addJob with sickBatch leaving batch on curBatches instead of oldBatches
• src/product/README.building.source
  • 1.16 lines changed: 18, context: html, text, full: html, text
    adding alternate path for minimal utilities
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.71 lines changed: 2, context: html, text, full: html, text
    v213 preview
• src/webBlat/webBlat.c
  • 1.10 lines changed: 2, context: html, text, full: html, text
    fixed comment mistake
  • 1.9 lines changed: 5, context: html, text, full: html, text
    use width 60 for protein codons, and 50 for nucleotides

• lines changed: 1938
• files changed: 57